Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds.

IF 6.3 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE
Boris Lukic, Ino Curik, Ivana Drzaic, Vlatko Galić, Mario Shihabi, Luboš Vostry, Vlatka Cubric-Curik
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Abstract

Background: The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type.

Results: We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis.

Conclusions: Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.

东亚得里亚海绵羊品种的选择、当地适应和生产类型特征的基因组特征。
背景:在亚得里亚海东部的地中海地区,绵羊繁殖的重要性自新石器时代迁徙以来就有着悠久的传统。绵羊生产系统是广泛的,通常在传统系统中进行,没有密集的系统育种计划来实现高统一性状的生产(胴体、羊毛和牛奶产量)。因此,八个来自亚得里亚海东部的克罗地亚本土绵羊品种在这里被视为集合种群(EAS),通常被认为是多用途品种(牛奶、肉和羊毛),不专门用于特定类型的生产,但以其健壮性和对某些环境条件的抵抗力而闻名。我们的目标是鉴定表现出阳性选择特征模式的基因组区域和基因,破译其生物学和生产功能,并提供EAS适应的“基因组”特征并确定其生产类型。结果:我们使用几种基于减少局部变异、连锁不平衡和位点频谱(eROHi、iHS、nSL和CLR)的方法在EAS中鉴定了正选择特征。我们的分析确定了许多与环境适应和经济重要性状相关的基因组区域和基因(例如桥粒钙粘蛋白和桥粒蛋白基因家族)。大多数候选基因与肉类/生产和健康/免疫反应性状有关,而发现的一些候选基因对驯化和进化过程很重要(例如,HOXa基因家族和FSIP2)。GO和QTL富集分析也证实了这些结果。结论:我们的研究结果有助于更好地理解EAS独特的适应性遗传结构,并确定其生产类型,最终为未来的育种计划提供了新的机会。同时,鉴定出的众多基因将提高我们对反刍动物(绵羊)在恶劣和特定地中海环境中的健壮性和抵抗力的理解。
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来源期刊
CiteScore
10.30
自引率
0.00%
发文量
822
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